Variant report

Variant	rs555156
Chromosome Location	chr11:84821981-84821982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10792792	0.88[CEU][hapmap]
rs10792794	0.92[CEU][hapmap]
rs10898336	0.88[CEU][hapmap]
rs10898343	0.88[CEU][hapmap]
rs10898350	1.00[JPT][hapmap]
rs10898360	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10898364	0.82[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1227842	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1227843	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs1237921	0.83[CEU][hapmap]
rs1238728	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1377303	1.00[CHB][hapmap]
rs1452928	0.92[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1823777	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.97[ASN][1000 genomes]
rs1826613	0.87[MKK][hapmap]
rs1940122	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs1940123	0.88[CEU][hapmap]
rs1940133	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs2155410	0.88[CEU][hapmap]
rs2155411	0.88[CEU][hapmap]
rs2155412	0.88[CEU][hapmap]
rs2253167	0.88[CEU][hapmap]
rs2444254	0.88[CEU][hapmap]
rs2444255	0.88[CEU][hapmap]
rs2453151	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2509053	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs2509056	0.81[CEU][hapmap]
rs2513242	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3862779	0.88[CEU][hapmap]
rs490286	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4944507	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs527389	0.88[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs540153	0.87[ASN][1000 genomes]
rs542892	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs543740	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs555259	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs560214	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs560587	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs567594	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs568330	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs568641	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs573650	0.90[CEU][hapmap]
rs574671	0.88[CEU][hapmap]
rs575189	0.88[CEU][hapmap]
rs577950	0.88[CEU][hapmap]
rs578782	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs582884	0.88[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs589093	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs592166	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs592622	0.96[CEU][hapmap];0.83[MEX][hapmap]
rs593800	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs594122	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs595435	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs596556	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs597592	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs601375	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs605652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607864	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs613265	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs613315	0.96[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs614689	0.92[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs617231	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs621007	0.88[CEU][hapmap]
rs625495	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs626013	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs626531	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs626700	0.92[CEU][hapmap]
rs630948	0.96[CEU][hapmap]
rs631370	0.88[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap]
rs632351	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs633562	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs635032	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs641655	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs641958	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs643891	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs646324	0.87[CEU][hapmap]
rs648506	0.83[EUR][1000 genomes]
rs649468	0.84[CEU][hapmap]
rs650374	0.92[CEU][hapmap]
rs651661	0.88[CEU][hapmap]
rs652830	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs658749	0.87[CEU][hapmap]
rs6592215	0.88[CEU][hapmap]
rs6592216	0.88[CEU][hapmap]
rs6592221	0.88[CEU][hapmap]
rs6592222	0.88[CEU][hapmap]
rs660274	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666735	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670998	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs675160	0.83[EUR][1000 genomes]
rs675217	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs675255	0.87[CEU][hapmap]
rs679745	0.96[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs685294	0.92[CEU][hapmap]
rs686009	1.00[CEU][hapmap]
rs687695	0.88[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs688329	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs689226	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs694142	0.84[CEU][hapmap]
rs7102107	0.85[CHB][hapmap];0.81[TSI][hapmap]
rs7110248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7118119	0.85[CHB][hapmap];0.81[TSI][hapmap]
rs7126522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7127990	0.88[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs7948646	0.82[CHB][hapmap];0.87[CHD][hapmap];0.83[MKK][hapmap];0.93[ASN][1000 genomes]
rs9634002	0.85[CHB][hapmap]
rs9634003	0.85[CHB][hapmap]
rs9634004	0.85[CHB][hapmap]
rs9634018	0.85[CHB][hapmap];0.85[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430415	chr11:84661652-84833852	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1040393	chr11:84708402-84866594	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv527535	chr11:84724795-84895033	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv528491	chr11:84724795-84895033	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1044370	chr11:84748993-85293233	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs555156	ANKRD42	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:84820000-84823200	Enhancers	Primary B cells from peripheral blood	blood
2	chr11:84821600-84822400	Flanking Active TSS	GM12878-XiMat	blood
3	chr11:84821600-84823000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr11:84821600-84825000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:84821800-84822400	Enhancers	Fetal Brain Female	brain
6	chr11:84821800-84822600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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